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Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta

This commit is contained in:
Alessia Bardi 2021-10-07 17:30:53 +02:00
parent 8d3b60f446 611ca511db
commit c48c43fa9e
34 changed files with 2985 additions and 502 deletions
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53
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/SparkDownloadUpdateDatacite.scala Normal file
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@ -0,0 +1,53 @@
package eu.dnetlib.dhp.actionmanager.datacite
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
import org.apache.hadoop.conf.Configuration
import org.apache.hadoop.fs.LocalFileSystem
import org.apache.hadoop.hdfs.DistributedFileSystem
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
import org.apache.spark.sql.functions.max
import org.slf4j.{Logger, LoggerFactory}
import java.text.SimpleDateFormat
import java.util.{Date, Locale}
import scala.io.Source
object SparkDownloadUpdateDatacite {
val log: Logger = LoggerFactory.getLogger(getClass)
def main(args: Array[String]): Unit = {
val conf = new SparkConf
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json")).mkString)
parser.parseArgument(args)
val master = parser.get("master")
val sourcePath = parser.get("sourcePath")
val workingPath = parser.get("workingPath")
val hdfsuri = parser.get("namenode")
log.info(s"namenode is $hdfsuri")
val spark: SparkSession = SparkSession.builder().config(conf)
.appName(getClass.getSimpleName)
.master(master)
.getOrCreate()
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val resEncoder: Encoder[Result] = Encoders.kryo[Result]
import spark.implicits._
val maxDate:String = spark.read.load(workingPath).as[Oaf].filter(s => s.isInstanceOf[Result]).map(r => r.asInstanceOf[Result].getDateofcollection).select(max("value")).first().getString(0)
val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US)
val string_to_date =ISO8601FORMAT.parse(maxDate)
val ts = string_to_date.getTime
}
}

154
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkWhitelistSimRels.java Normal file
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package eu.dnetlib.dhp.oa.dedup;
import java.io.IOException;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.dom4j.DocumentException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.xml.sax.SAXException;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.model.MapDocument;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
public class SparkWhitelistSimRels extends AbstractSparkAction {
private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class);
private static final String WHITELIST_SEPARATOR = "####";
public SparkWhitelistSimRels(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark);
}
public static void main(String[] args) throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkCreateSimRels.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json")));
parser.parseArgument(args);
SparkConf conf = new SparkConf();
new SparkWhitelistSimRels(parser, getSparkSession(conf))
.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
}
@Override
public void run(ISLookUpService isLookUpService)
throws DocumentException, IOException, ISLookUpException, SAXException {
// read oozie parameters
final String graphBasePath = parser.get("graphBasePath");
final String isLookUpUrl = parser.get("isLookUpUrl");
final String actionSetId = parser.get("actionSetId");
final String workingPath = parser.get("workingPath");
final int numPartitions = Optional
.ofNullable(parser.get("numPartitions"))
.map(Integer::valueOf)
.orElse(NUM_PARTITIONS);
final String whiteListPath = parser.get("whiteListPath");
log.info("numPartitions: '{}'", numPartitions);
log.info("graphBasePath: '{}'", graphBasePath);
log.info("isLookUpUrl: '{}'", isLookUpUrl);
log.info("actionSetId: '{}'", actionSetId);
log.info("workingPath: '{}'", workingPath);
log.info("whiteListPath: '{}'", whiteListPath);
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
// file format: source####target
Dataset<Tuple2<String, String>> whiteListRels = spark
.createDataset(
sc
.textFile(whiteListPath)
// check if the line is in the correct format: id1####id2
.filter(s -> s.contains(WHITELIST_SEPARATOR) && s.split(WHITELIST_SEPARATOR).length == 2)
.map(s -> new Tuple2<>(s.split(WHITELIST_SEPARATOR)[0], s.split(WHITELIST_SEPARATOR)[1]))
.rdd(),
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
// for each dedup configuration
for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) {
final String entity = dedupConf.getWf().getEntityType();
final String subEntity = dedupConf.getWf().getSubEntityValue();
log.info("Adding whitelist simrels for: '{}'", subEntity);
final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity);
Dataset<Tuple2<String, String>> entities = spark
.createDataset(
sc
.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
.repartition(numPartitions)
.mapToPair(
(PairFunction<String, String, String>) s -> {
MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
return new Tuple2<>(d.getIdentifier(), "present");
})
.rdd(),
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
Dataset<Tuple2<String, String>> whiteListRels1 = whiteListRels
.joinWith(entities, whiteListRels.col("_1").equalTo(entities.col("_1")), "inner")
.map(
(MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, String>>, Tuple2<String, String>>) Tuple2::_1,
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
Dataset<Tuple2<String, String>> whiteListRels2 = whiteListRels1
.joinWith(entities, whiteListRels1.col("_2").equalTo(entities.col("_1")), "inner")
.map(
(MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, String>>, Tuple2<String, String>>) Tuple2::_1,
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
Dataset<Relation> whiteListSimRels = whiteListRels2
.map(
(MapFunction<Tuple2<String, String>, Relation>) r -> createSimRel(r._1(), r._2(), entity),
Encoders.bean(Relation.class));
saveParquet(whiteListSimRels, outputPath, SaveMode.Append);
}
}
private Relation createSimRel(String source, String target, String entity) {
final Relation r = new Relation();
r.setSource(source);
r.setTarget(target);
r.setSubRelType("dedupSimilarity");
r.setRelClass("isSimilarTo");
r.setDataInfo(new DataInfo());
switch (entity) {
case "result":
r.setRelType("resultResult");
break;
case "organization":
r.setRelType("organizationOrganization");
break;
default:
throw new IllegalArgumentException("unmanaged entity type: " + entity);
}
return r;
}
}

117
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/UpdateOpenorgsJob.java Normal file
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@ -0,0 +1,117 @@
package eu.dnetlib.dhp.oa.dedup;
import java.util.concurrent.TimeUnit;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class UpdateOpenorgsJob {
private static final Logger log = LoggerFactory.getLogger(UpdateOpenorgsJob.class);
public static void main(String[] args) throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkCreateSimRels.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/updateOpenorgsJob_parameters.json")));
parser.parseArgument(args);
final String apiUrl = parser.get("apiUrl");
final int delay = Integer.parseInt(parser.get("delay"));
log.info("apiUrl: '{}'", apiUrl);
log.info("delay: '{}'", delay);
APIResponse res = httpCall(apiUrl);
while (res != null && res.getStatus().equals(ImportStatus.RUNNING)) {
TimeUnit.MINUTES.sleep(delay);
res = httpCall(apiUrl + "/status");
}
if (res == null) {
log.error("Openorgs Update FAILED: No response");
throw new RuntimeException("Openorgs Update FAILED: No response");
}
if (res.getStatus() == null || !res.getStatus().equals(ImportStatus.SUCCESS)) {
log.error("Openorgs Update FAILED: '{}' - '{}'", res.getStatus(), res.getMessage());
throw new RuntimeException(res.getMessage());
}
}
private static APIResponse httpCall(final String url) throws Exception {
final HttpGet req = new HttpGet(url);
try (final CloseableHttpClient client = HttpClients.createDefault()) {
try (final CloseableHttpResponse response = client.execute(req)) {
final String s = IOUtils.toString(response.getEntity().getContent());
return (new ObjectMapper()).readValue(s, APIResponse.class);
}
}
}
}
class APIResponse {
private String id;
private Long dateStart;
private Long dateEnd;
private ImportStatus status;
private String message;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public Long getDateStart() {
return dateStart;
}
public void setDateStart(Long dateStart) {
this.dateStart = dateStart;
}
public Long getDateEnd() {
return dateEnd;
}
public void setDateEnd(Long dateEnd) {
this.dateEnd = dateEnd;
}
public ImportStatus getStatus() {
return status;
}
public void setStatus(ImportStatus status) {
this.status = status;
}
public String getMessage() {
return message;
}
public void setMessage(String message) {
this.message = message;
}
}
enum ImportStatus {
SUCCESS, FAILED, RUNNING, NOT_LAUNCHED, NOT_YET_STARTED
}

26
dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/workflow.xml
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@ -28,6 +28,11 @@
<name>dbPwd</name> <name>dbPwd</name>
<description>password to access the OpenOrgs database</description> <description>password to access the OpenOrgs database</description>
</property> </property>
<property>
<name>dbConnections</name>
<value>10</value>
<description>number of connections to the postgres db</description>
</property>
<property> <property>
<name>workingPath</name> <name>workingPath</name>
<description>path for the working directory</description> <description>path for the working directory</description>
@ -223,7 +228,7 @@
<arg>--dbTable</arg><arg>${dbTable}</arg> <arg>--dbTable</arg><arg>${dbTable}</arg>
<arg>--dbUser</arg><arg>${dbUser}</arg> <arg>--dbUser</arg><arg>${dbUser}</arg>
<arg>--dbPwd</arg><arg>${dbPwd}</arg> <arg>--dbPwd</arg><arg>${dbPwd}</arg>
<arg>--numConnections</arg><arg>20</arg> <arg>--numConnections</arg><arg>${dbConnections}</arg>
</spark> </spark>
<ok to="PrepareNewOrgs"/> <ok to="PrepareNewOrgs"/>
<error to="Kill"/> <error to="Kill"/>
@ -254,19 +259,24 @@
<arg>--dbTable</arg><arg>${dbTable}</arg> <arg>--dbTable</arg><arg>${dbTable}</arg>
<arg>--dbUser</arg><arg>${dbUser}</arg> <arg>--dbUser</arg><arg>${dbUser}</arg>
<arg>--dbPwd</arg><arg>${dbPwd}</arg> <arg>--dbPwd</arg><arg>${dbPwd}</arg>
<arg>--numConnections</arg><arg>20</arg> <arg>--numConnections</arg><arg>${dbConnections}</arg>
</spark> </spark>
<ok to="update_openorgs"/> <ok to="update_openorgs"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>
<action name="update_openorgs"> <action name="update_openorgs">
<shell xmlns="uri:oozie:shell-action:0.1"> <java>
<job-tracker>${jobTracker}</job-tracker> <configuration>
<name-node>${nameNode}</name-node> <property>
<exec>/usr/bin/curl</exec> <name>oozie.launcher.mapreduce.user.classpath.first</name>
<argument>${apiUrl}</argument> <value>true</value>
</shell> </property>
</configuration>
<main-class>eu.dnetlib.dhp.oa.dedup.UpdateOpenorgsJob</main-class>
<arg>--apiUrl</arg><arg>${apiUrl}</arg>
<arg>--delay</arg><arg>5</arg>
</java>
<ok to="End"/> <ok to="End"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>

32
dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml
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@ -20,6 +20,10 @@
<name>workingPath</name> <name>workingPath</name>
<description>path for the working directory</description> <description>path for the working directory</description>
</property> </property>
<property>
<name>whiteListPath</name>
<description>path for the whitelist of similarity relations</description>
</property>
<property> <property>
<name>dedupGraphPath</name> <name>dedupGraphPath</name>
<description>path for the output graph</description> <description>path for the output graph</description>
@ -130,6 +134,34 @@
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--numPartitions</arg><arg>8000</arg> <arg>--numPartitions</arg><arg>8000</arg>
</spark> </spark>
<ok to="WhitelistSimRels"/>
<error to="Kill"/>
</action>
<action name="WhitelistSimRels">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Add Whitelist Similarity Relations</name>
<class>eu.dnetlib.dhp.oa.dedup.SparkWhitelistSimRels</class>
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--whiteListPath</arg><arg>${whiteListPath}</arg>
<arg>--numPartitions</arg><arg>8000</arg>
</spark>
<ok to="CreateMergeRel"/> <ok to="CreateMergeRel"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>

14
dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/updateOpenorgsJob_parameters.json Normal file
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@ -0,0 +1,14 @@
[
{
"paramName": "api",
"paramLongName": "apiUrl",
"paramDescription": "the url of the API",
"paramRequired": true
},
{
"paramName": "d",
"paramLongName": "delay",
"paramDescription": "delay for the HTTP call in minutes",
"paramRequired": true
}
]

38
dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json Normal file
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@ -0,0 +1,38 @@
[
{
"paramName": "la",
"paramLongName": "isLookUpUrl",
"paramDescription": "address for the LookUp",
"paramRequired": true
},
{
"paramName": "asi",
"paramLongName": "actionSetId",
"paramDescription": "action set identifier (name of the orchestrator)",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "graphBasePath",
"paramDescription": "the base path of the raw graph",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingPath",
"paramDescription": "path of the working directory",
"paramRequired": true
},
{
"paramName": "np",
"paramLongName": "numPartitions",
"paramDescription": "number of partitions for the similarity relations intermediate phases",
"paramRequired": false
},
{
"paramName": "wl",
"paramLongName": "whiteListPath",
"paramDescription": "whitelist file path for the addition of custom simrels",
"paramRequired": true
}
]

105
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
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@ -5,13 +5,16 @@ import static java.nio.file.Files.createTempDirectory;
import static org.apache.spark.sql.functions.count; import static org.apache.spark.sql.functions.count;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.Mockito.lenient; import static org.mockito.Mockito.lenient;
import java.io.File; import java.io.File;
import java.io.FileReader;
import java.io.IOException; import java.io.IOException;
import java.io.Serializable; import java.io.Serializable;
import java.net.URISyntaxException; import java.net.URISyntaxException;
import java.nio.file.Paths; import java.nio.file.Paths;
import java.util.List;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
@ -55,6 +58,10 @@ public class SparkDedupTest implements Serializable {
private static String testOutputBasePath; private static String testOutputBasePath;
private static String testDedupGraphBasePath; private static String testDedupGraphBasePath;
private static final String testActionSetId = "test-orchestrator"; private static final String testActionSetId = "test-orchestrator";
private static String whitelistPath;
private static List<String> whiteList;
private static String WHITELIST_SEPARATOR = "####";
@BeforeAll @BeforeAll
public static void cleanUp() throws IOException, URISyntaxException { public static void cleanUp() throws IOException, URISyntaxException {
@ -71,6 +78,12 @@ public class SparkDedupTest implements Serializable {
.toAbsolutePath() .toAbsolutePath()
.toString(); .toString();
whitelistPath = Paths
.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/whitelist.simrels.txt").toURI())
.toFile()
.getAbsolutePath();
whiteList = IOUtils.readLines(new FileReader(whitelistPath));
FileUtils.deleteDirectory(new File(testOutputBasePath)); FileUtils.deleteDirectory(new File(testOutputBasePath));
FileUtils.deleteDirectory(new File(testDedupGraphBasePath)); FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
@ -202,6 +215,84 @@ public class SparkDedupTest implements Serializable {
@Test @Test
@Order(2) @Order(2)
void whitelistSimRelsTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkWhitelistSimRels.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json")));
parser
.parseArgument(
new String[] {
"-i", testGraphBasePath,
"-asi", testActionSetId,
"-la", "lookupurl",
"-w", testOutputBasePath,
"-np", "50",
"-wl", whitelistPath
});
new SparkWhitelistSimRels(parser, spark).run(isLookUpService);
long orgs_simrel = spark
.read()
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
.count();
long pubs_simrel = spark
.read()
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "publication"))
.count();
long ds_simrel = spark
.read()
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "dataset"))
.count();
long orp_simrel = spark
.read()
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "otherresearchproduct"))
.count();
// entities simrels supposed to be equal to the number of previous step (no rels in whitelist)
assertEquals(3082, orgs_simrel);
assertEquals(7036, pubs_simrel);
assertEquals(442, ds_simrel);
assertEquals(6750, orp_simrel);
// entities simrels to be different from the number of previous step (new simrels in the whitelist)
Dataset<Row> sw_simrel = spark
.read()
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "software"));
// check if the first relation in the whitelist exists
assertTrue(
sw_simrel
.as(Encoders.bean(Relation.class))
.toJavaRDD()
.filter(
rel -> rel.getSource().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[0])
&& rel.getTarget().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[1]))
.count() > 0);
// check if the second relation in the whitelist exists
assertTrue(
sw_simrel
.as(Encoders.bean(Relation.class))
.toJavaRDD()
.filter(
rel -> rel.getSource().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[0])
&& rel.getTarget().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[1]))
.count() > 0);
assertEquals(338, sw_simrel.count());
}
@Test
@Order(3)
void cutMergeRelsTest() throws Exception { void cutMergeRelsTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser( ArgumentApplicationParser parser = new ArgumentApplicationParser(
@ -297,7 +388,7 @@ public class SparkDedupTest implements Serializable {
} }
@Test @Test
@Order(3) @Order(4)
void createMergeRelsTest() throws Exception { void createMergeRelsTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser( ArgumentApplicationParser parser = new ArgumentApplicationParser(
@ -353,7 +444,7 @@ public class SparkDedupTest implements Serializable {
} }
@Test @Test
@Order(4) @Order(5)
void createDedupRecordTest() throws Exception { void createDedupRecordTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser( ArgumentApplicationParser parser = new ArgumentApplicationParser(
@ -394,13 +485,13 @@ public class SparkDedupTest implements Serializable {
assertEquals(85, orgs_deduprecord); assertEquals(85, orgs_deduprecord);
assertEquals(65, pubs_deduprecord); assertEquals(65, pubs_deduprecord);
assertEquals(51, sw_deduprecord); assertEquals(49, sw_deduprecord);
assertEquals(97, ds_deduprecord); assertEquals(97, ds_deduprecord);
assertEquals(89, orp_deduprecord); assertEquals(89, orp_deduprecord);
} }
@Test @Test
@Order(5) @Order(6)
void updateEntityTest() throws Exception { void updateEntityTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser( ArgumentApplicationParser parser = new ArgumentApplicationParser(
@ -479,7 +570,7 @@ public class SparkDedupTest implements Serializable {
assertEquals(838, organizations); assertEquals(838, organizations);
assertEquals(100, projects); assertEquals(100, projects);
assertEquals(100, datasource); assertEquals(100, datasource);
assertEquals(200, softwares); assertEquals(198, softwares);
assertEquals(389, dataset); assertEquals(389, dataset);
assertEquals(517, otherresearchproduct); assertEquals(517, otherresearchproduct);
@ -516,7 +607,7 @@ public class SparkDedupTest implements Serializable {
} }
@Test @Test
@Order(6) @Order(7)
void propagateRelationTest() throws Exception { void propagateRelationTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser( ArgumentApplicationParser parser = new ArgumentApplicationParser(
@ -566,7 +657,7 @@ public class SparkDedupTest implements Serializable {
} }
@Test @Test
@Order(7) @Order(8)
void testRelations() throws Exception { void testRelations() throws Exception {
testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_1.json", 12, 10); testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_1.json", 12, 10);
testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_2.json", 10, 2); testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_2.json", 10, 2);

2
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/whitelist.simrels.txt Normal file
View File

@ -0,0 +1,2 @@
50|r37b0ad08687::f645b9729d1e1025a72c57883f0f2cac####50|r37b0ad08687::4c55b436743b5c49fa32cd582fd9e1aa
50|datacite____::a90f49f9fde5393c00633bea6e4e374a####50|datacite____::5f55cdee77303ba8a2bf9996c32a330c

51
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala
View File

@ -13,10 +13,30 @@ import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory} import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._ import scala.collection.JavaConverters._
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString,JArray}
import org.json4s.jackson.JsonMethods.parse
object SparkGenerateDoiBoost { object SparkGenerateDoiBoost {
def extractIdGRID(input:String):List[(String,String)] = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: org.json4s.JValue = parse(input)
val id:String = (json \ "id").extract[String]
val grids:List[String] = for {
JObject(pid) <- json \ "pid"
JField("qualifier", JObject(qualifier)) <- pid
JField("classid", JString(classid)) <-qualifier
JField("value", JString(vl)) <- pid
if classid == "GRID"
} yield vl
grids.map(g => (id, s"unresolved::grid::${g.toLowerCase}"))(collection.breakOut)
}
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {
@ -36,6 +56,7 @@ object SparkGenerateDoiBoost {
val hostedByMapPath = parser.get("hostedByMapPath") val hostedByMapPath = parser.get("hostedByMapPath")
val workingDirPath = parser.get("workingPath") val workingDirPath = parser.get("workingPath")
val openaireOrganizationPath = parser.get("openaireOrganizationPath")
val crossrefAggregator = new Aggregator[(String, Publication), Publication, Publication] with Serializable { val crossrefAggregator = new Aggregator[(String, Publication), Publication, Publication] with Serializable {
override def zero: Publication = new Publication override def zero: Publication = new Publication
@ -156,7 +177,7 @@ object SparkGenerateDoiBoost {
magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).flatMap(item => { magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).flatMap(item => {
val pub:Publication = item._1._2 val pub:Publication = item._1._2
val affiliation = item._2 val affiliation = item._2
val affId:String = if (affiliation.GridId.isDefined) DoiBoostMappingUtil.generateGridAffiliationId(affiliation.GridId.get) else DoiBoostMappingUtil.generateMAGAffiliationId(affiliation.AffiliationId.toString) val affId:String = if (affiliation.GridId.isDefined) s"unresolved::grid::${affiliation.GridId.get.toLowerCase}" else DoiBoostMappingUtil.generateMAGAffiliationId(affiliation.AffiliationId.toString)
val r:Relation = new Relation val r:Relation = new Relation
r.setSource(pub.getId) r.setSource(pub.getId)
r.setTarget(affId) r.setTarget(affId)
@ -174,9 +195,35 @@ object SparkGenerateDoiBoost {
r1.setDataInfo(pub.getDataInfo) r1.setDataInfo(pub.getDataInfo)
r1.setCollectedfrom(List(DoiBoostMappingUtil.createMAGCollectedFrom()).asJava) r1.setCollectedfrom(List(DoiBoostMappingUtil.createMAGCollectedFrom()).asJava)
List(r, r1) List(r, r1)
})(mapEncoderRel).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation") })(mapEncoderRel).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation_unresolved")
val unresolvedRels:Dataset[(String, Relation)] = spark.read.load(s"$workingDirPath/doiBoostPublicationAffiliation_unresolved").as[Relation].map(r => {
if (r.getSource.startsWith("unresolved"))
(r.getSource, r)
else if (r.getTarget.startsWith("unresolved"))
(r.getTarget,r)
else
("resolved", r)
})
val openaireOrganization:Dataset[(String,String)] = spark.read.text(openaireOrganizationPath).as[String].flatMap(s => extractIdGRID(s)).groupByKey(_._2).reduceGroups((x,y) => if (x != null) x else y ).map(_._2)
unresolvedRels.joinWith(openaireOrganization,unresolvedRels("_1").equalTo(openaireOrganization("_2")))
.map { x =>
val currentRels = x._1._2
val currentOrgs = x._2
if (currentOrgs!= null)
if(currentRels.getSource.startsWith("unresolved"))
currentRels.setSource(currentOrgs._1)
else
currentRels.setTarget(currentOrgs._1)
currentRels
}.write.save(s"$workingDirPath/doiBoostPublicationAffiliation")
magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).map( item => { magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).map( item => {
val affiliation = item._2 val affiliation = item._2
if (affiliation.GridId.isEmpty) { if (affiliation.GridId.isEmpty) {

3
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json
View File

@ -1,7 +1,8 @@
[ [
{"paramName": "m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true}, {"paramName": "m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true},
{"paramName": "hb", "paramLongName":"hostedByMapPath", "paramDescription": "the hosted By Map Path", "paramRequired": true}, {"paramName": "hb", "paramLongName":"hostedByMapPath", "paramDescription": "the hosted By Map Path", "paramRequired": true},
{"paramName": "oo", "paramLongName":"openaireOrganizationPath", "paramDescription": "the openaire Organization Path", "paramRequired": true},
{"paramName": "ap", "paramLongName":"affiliationPath", "paramDescription": "the Affliation Path", "paramRequired": true}, {"paramName": "ap", "paramLongName":"affiliationPath", "paramDescription": "the Affliation Path", "paramRequired": true},
{"paramName": "pa", "paramLongName":"paperAffiliationPath", "paramDescription": "the paperAffiliation Path", "paramRequired": true}, {"paramName": "pa", "paramLongName":"paperAffiliationPath", "paramDescription": "the paperAffiliation Path", "paramRequired": true},
{"paramName": "w", "paramLongName":"workingPath", "paramDescription": "the Working Path", "paramRequired": true} {"paramName": "w", "paramLongName":"workingPath", "paramDescription": "the Working Path", "paramRequired": true}
] ]

7
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml
View File

@ -27,6 +27,12 @@
<name>hostedByMapPath</name> <name>hostedByMapPath</name>
<description>the hostedByMap Path</description> <description>the hostedByMap Path</description>
</property> </property>
<property>
<name>openaireOrganizationPath</name>
<description>the OpenAire Organizations Path</description>
</property>
<property> <property>
<name>outputPath</name> <name>outputPath</name>
<description>the Path of the sequence file action set</description> <description>the Path of the sequence file action set</description>
@ -214,6 +220,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts> </spark-opts>
<arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg> <arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg>
<arg>--openaireOrganizationPath</arg><arg>${openaireOrganizationPath}</arg>
<arg>--affiliationPath</arg><arg>${inputPathMAG}/dataset/Affiliations</arg> <arg>--affiliationPath</arg><arg>${inputPathMAG}/dataset/Affiliations</arg>
<arg>--paperAffiliationPath</arg><arg>${inputPathMAG}/dataset/PaperAuthorAffiliations</arg> <arg>--paperAffiliationPath</arg><arg>${inputPathMAG}/dataset/PaperAuthorAffiliations</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingPath</arg><arg>${workingPath}</arg>

123
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkCreateBaselineDataFrame.scala
View File

@ -6,18 +6,130 @@ import eu.dnetlib.dhp.schema.oaf.Result
import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf} import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
import eu.dnetlib.dhp.utils.ISLookupClientFactory import eu.dnetlib.dhp.utils.ISLookupClientFactory
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
import org.apache.hadoop.conf.Configuration
import org.apache.hadoop.fs.{FSDataOutputStream, FileSystem, Path}
import org.apache.http.client.config.RequestConfig
import org.apache.http.client.methods.HttpGet
import org.apache.http.impl.client.HttpClientBuilder
import org.apache.spark.SparkConf import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD import org.apache.spark.rdd.RDD
import org.apache.spark.sql.expressions.Aggregator import org.apache.spark.sql.expressions.Aggregator
import org.apache.spark.sql._ import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory} import org.slf4j.{Logger, LoggerFactory}
import java.io.InputStream
import scala.io.Source import scala.io.Source
import scala.xml.pull.XMLEventReader import scala.xml.pull.XMLEventReader
object SparkCreateBaselineDataFrame { object SparkCreateBaselineDataFrame {
def requestBaseLineUpdatePage(maxFile:String):List[(String,String)] = {
val data =requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/")
val result =data.lines.filter(l => l.startsWith("<a href=")).map{l =>
val end = l.lastIndexOf("\">")
val start = l.indexOf("<a href=\"")
if (start>= 0 && end >start)
l.substring(start+9, (end-start))
else
""
}.filter(s =>s.endsWith(".gz") ).filter(s => s > maxFile).map(s => (s,s"https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/$s")).toList
result
}
def downloadBaselinePart(url:String):InputStream = {
val r = new HttpGet(url)
val timeout = 60; // seconds
val config = RequestConfig.custom()
.setConnectTimeout(timeout * 1000)
.setConnectionRequestTimeout(timeout * 1000)
.setSocketTimeout(timeout * 1000).build()
val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build()
val response = client.execute(r)
println(s"get response with status${response.getStatusLine.getStatusCode}")
response.getEntity.getContent
}
def requestPage(url:String):String = {
val r = new HttpGet(url)
val timeout = 60; // seconds
val config = RequestConfig.custom()
.setConnectTimeout(timeout * 1000)
.setConnectionRequestTimeout(timeout * 1000)
.setSocketTimeout(timeout * 1000).build()
val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build()
try {
var tries = 4
while (tries > 0) {
println(s"requesting ${r.getURI}")
try {
val response = client.execute(r)
println(s"get response with status${response.getStatusLine.getStatusCode}")
if (response.getStatusLine.getStatusCode > 400) {
tries -= 1
}
else
return IOUtils.toString(response.getEntity.getContent)
} catch {
case e: Throwable =>
println(s"Error on requesting ${r.getURI}")
e.printStackTrace()
tries -= 1
}
}
""
} finally {
if (client != null)
client.close()
}
}
def downloadBaseLineUpdate(baselinePath:String, hdfsServerUri:String ):Unit = {
val conf = new Configuration
conf.set("fs.defaultFS", hdfsServerUri)
val fs = FileSystem.get(conf)
val p = new Path(baselinePath)
val files = fs.listFiles(p,false)
var max_file = ""
while (files.hasNext) {
val c = files.next()
val data = c.getPath.toString
val fileName = data.substring(data.lastIndexOf("/")+1)
if (fileName> max_file)
max_file = fileName
}
val files_to_download = requestBaseLineUpdatePage(max_file)
files_to_download.foreach { u =>
val hdfsWritePath: Path = new Path(s"$baselinePath/${u._1}")
val fsDataOutputStream: FSDataOutputStream = fs.create(hdfsWritePath, true)
val i = downloadBaselinePart(u._2)
val buffer = Array.fill[Byte](1024)(0)
while(i.read(buffer)>0) {
fsDataOutputStream.write(buffer)
}
i.close()
println(s"Downloaded ${u._2} into $baselinePath/${u._1}")
fsDataOutputStream.close()
}
}
val pmArticleAggregator: Aggregator[(String, PMArticle), PMArticle, PMArticle] = new Aggregator[(String, PMArticle), PMArticle, PMArticle] with Serializable { val pmArticleAggregator: Aggregator[(String, PMArticle), PMArticle, PMArticle] = new Aggregator[(String, PMArticle), PMArticle, PMArticle] with Serializable {
override def zero: PMArticle = new PMArticle override def zero: PMArticle = new PMArticle
@ -51,6 +163,10 @@ object SparkCreateBaselineDataFrame {
val targetPath = parser.get("targetPath") val targetPath = parser.get("targetPath")
log.info("targetPath: {}", targetPath) log.info("targetPath: {}", targetPath)
val hdfsServerUri = parser.get("hdfsServerUri")
log.info("hdfsServerUri: {}", targetPath)
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl) val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService) val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
val spark: SparkSession = val spark: SparkSession =
@ -61,16 +177,15 @@ object SparkCreateBaselineDataFrame {
.master(parser.get("master")).getOrCreate() .master(parser.get("master")).getOrCreate()
import spark.implicits._ import spark.implicits._
val sc = spark.sparkContext val sc = spark.sparkContext
implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle]) implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle])
implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal]) implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal])
implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor]) implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor])
implicit val resultEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) implicit val resultEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
downloadBaseLineUpdate(s"$workingPath/baseline", hdfsServerUri)
val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline",2000) val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline",2000)
val ds:Dataset[PMArticle] = spark.createDataset(k.filter(i => i._1.endsWith(".gz")).flatMap(i =>{ val ds:Dataset[PMArticle] = spark.createDataset(k.filter(i => i._1.endsWith(".gz")).flatMap(i =>{
val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes())) val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
@ -87,7 +202,5 @@ object SparkCreateBaselineDataFrame {
.map(a => PubMedToOaf.convert(a, vocabularies)).as[Result] .map(a => PubMedToOaf.convert(a, vocabularies)).as[Result]
.filter(p => p!= null) .filter(p => p!= null)
.write.mode(SaveMode.Overwrite).save(targetPath) .write.mode(SaveMode.Overwrite).save(targetPath)
//s"$workingPath/oaf/baseline_oaf"
} }
} }

71
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkDownloadEBILinks.scala
View File

@ -5,17 +5,15 @@ import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.EBILinkItem
import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal} import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
import org.apache.http.client.config.RequestConfig import org.apache.http.client.config.RequestConfig
import org.apache.http.client.methods.{HttpGet, HttpUriRequest} import org.apache.http.client.methods.HttpGet
import org.apache.http.impl.client.HttpClientBuilder import org.apache.http.impl.client.HttpClientBuilder
import org.apache.spark.SparkConf import org.apache.spark.SparkConf
import org.apache.spark.sql.expressions.Aggregator
import org.apache.spark.sql.functions.max import org.apache.spark.sql.functions.max
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory} import org.slf4j.{Logger, LoggerFactory}
object SparkDownloadEBILinks { object SparkDownloadEBILinks {
def createEBILinks(pmid:Long):EBILinkItem = { def createEBILinks(pmid:Long):EBILinkItem = {
val res = requestLinks(pmid) val res = requestLinks(pmid)
@ -24,39 +22,42 @@ object SparkDownloadEBILinks {
null null
} }
def requestPage(url:String):String = {
val r = new HttpGet(url)
val timeout = 60; // seconds
val config = RequestConfig.custom()
.setConnectTimeout(timeout * 1000)
.setConnectionRequestTimeout(timeout * 1000)
.setSocketTimeout(timeout * 1000).build()
val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build()
try {
var tries = 4
while (tries > 0) {
println(s"requesting ${r.getURI}")
try {
val response = client.execute(r)
println(s"get response with status${response.getStatusLine.getStatusCode}")
if (response.getStatusLine.getStatusCode > 400) {
tries -= 1
}
else
return IOUtils.toString(response.getEntity.getContent)
} catch {
case e: Throwable =>
println(s"Error on requesting ${r.getURI}")
e.printStackTrace()
tries -= 1
}
}
""
} finally {
if (client != null)
client.close()
}
}
def requestLinks(PMID:Long):String = { def requestLinks(PMID:Long):String = {
val r = new HttpGet(s"https://www.ebi.ac.uk/europepmc/webservices/rest/MED/$PMID/datalinks?format=json") requestPage(s"https://www.ebi.ac.uk/europepmc/webservices/rest/MED/$PMID/datalinks?format=json")
val timeout = 60; // seconds
val config = RequestConfig.custom()
.setConnectTimeout(timeout * 1000)
.setConnectionRequestTimeout(timeout * 1000)
.setSocketTimeout(timeout * 1000).build()
val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build()
try {
var tries = 4
while (tries > 0) {
println(s"requesting ${r.getURI}")
try {
val response = client.execute(r)
println(s"get response with status${response.getStatusLine.getStatusCode}")
if (response.getStatusLine.getStatusCode > 400) {
tries -= 1
}
else
return IOUtils.toString(response.getEntity.getContent)
} catch {
case e: Throwable =>
println(s"Error on requesting ${r.getURI}")
e.printStackTrace()
tries -= 1
}
}
""
} finally {
if (client != null)
client.close()
}
} }
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {

5
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkEBILinksToOaf.scala
View File

@ -32,14 +32,9 @@ object SparkEBILinksToOaf {
import spark.implicits._ import spark.implicits._
implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
val ebi_rdd:Dataset[EBILinkItem] = spark.createDataset(spark.sparkContext.textFile(sourcePath).map(s => BioDBToOAF.extractEBILinksFromDump(s))).as[EBILinkItem]
ebi_rdd.write.mode(SaveMode.Overwrite).save(s"${sourcePath}_dataset")
val ebLinks:Dataset[EBILinkItem] = spark.read.load(s"${sourcePath}_dataset").as[EBILinkItem].filter(l => l.links!= null) val ebLinks:Dataset[EBILinkItem] = spark.read.load(s"${sourcePath}_dataset").as[EBILinkItem].filter(l => l.links!= null)
ebLinks.flatMap(j =>BioDBToOAF.parse_ebi_links(j.links)) ebLinks.flatMap(j =>BioDBToOAF.parse_ebi_links(j.links))
.repartition(4000)
.filter(p => BioDBToOAF.EBITargetLinksFilter(p)) .filter(p => BioDBToOAF.EBITargetLinksFilter(p))
.flatMap(p => BioDBToOAF.convertEBILinksToOaf(p)) .flatMap(p => BioDBToOAF.convertEBILinksToOaf(p))
.write.mode(SaveMode.Overwrite).save(targetPath) .write.mode(SaveMode.Overwrite).save(targetPath)

8
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/lib/scripts/postprocessing.sql
View File

@ -1,10 +1,10 @@
DROP VIEW IF EXISTS ${hiveDbName}.result; DROP VIEW IF EXISTS ${hiveDbName}.result;
CREATE VIEW IF NOT EXISTS ${hiveDbName}.result as CREATE VIEW IF NOT EXISTS ${hiveDbName}.result as
select id, originalid, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.publication p select id, originalid, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance, measures from ${hiveDbName}.publication p
union all union all
select id, originalid, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.dataset d select id, originalid, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance, measures from ${hiveDbName}.dataset d
union all union all
select id, originalid, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.software s select id, originalid, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance, measures from ${hiveDbName}.software s
union all union all
select id, originalid, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.otherresearchproduct o; select id, originalid, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance, measures from ${hiveDbName}.otherresearchproduct o;

9
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json
View File

@ -1,6 +1,7 @@
[ [
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"i", "paramLongName":"isLookupUrl","paramDescription": "isLookupUrl", "paramRequired": true}, {"paramName":"i", "paramLongName":"isLookupUrl", "paramDescription": "isLookupUrl", "paramRequired": true},
{"paramName":"w", "paramLongName":"workingPath","paramDescription": "the path of the sequencial file to read", "paramRequired": true}, {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true},
{"paramName":"t", "paramLongName":"targetPath","paramDescription": "the oaf path ", "paramRequired": true} {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the oaf path ", "paramRequired": true},
{"paramName":"h", "paramLongName":"hdfsServerUri", "paramDescription": "the working path ", "paramRequired": true}
] ]

6
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/ebi_download_update.json
View File

@ -1,5 +1,5 @@
[ [
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"s", "paramLongName":"sourcePath","paramDescription": "the source Path", "paramRequired": true}, {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true},
{"paramName":"w", "paramLongName":"workingPath","paramDescription": "the working path ", "paramRequired": true} {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working path ", "paramRequired": true}
] ]

4
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/workflow.xml
View File

@ -25,7 +25,6 @@
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message> <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill> </kill>
<action name="GenerateBaselineDataset"> <action name="GenerateBaselineDataset">
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master> <master>yarn-cluster</master>
@ -43,6 +42,7 @@
</spark-opts> </spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn</arg> <arg>--master</arg><arg>yarn</arg>
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
</spark> </spark>
<ok to="End"/> <ok to="End"/>
<error to="Kill"/> <error to="Kill"/>
@ -74,7 +74,7 @@
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master> <master>yarn-cluster</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Create Baselnie DataSet</name> <name>Create Baseline DataSet</name>
<class>eu.dnetlib.dhp.sx.ebi.SparkAddLinkUpdates</class> <class>eu.dnetlib.dhp.sx.ebi.SparkAddLinkUpdates</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>

116
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/workflow.xml
View File

@ -1,59 +1,67 @@
<workflow-app name="Create EBI Dataset" xmlns="uri:oozie:workflow:0.5"> <workflow-app name="Create EBI Dataset" xmlns="uri:oozie:workflow:0.5">
<parameters> <parameters>
<property> <property>
<name>sourcePath</name> <name>sourcePath</name>
<description>the Working Path</description> <description>the Working Path</description>
</property> </property>
<property> <property>
<name>workingPath</name> <name>workingPath</name>
<description>the Working Path</description> <description>the Working Path</description>
</property> </property>
<property> <property>
<name>sparkDriverMemory</name> <name>sparkDriverMemory</name>
<description>memory for driver process</description> <description>memory for driver process</description>
</property> </property>
<property> <property>
<name>sparkExecutorMemory</name> <name>sparkExecutorMemory</name>
<description>memory for individual executor</description> <description>memory for individual executor</description>
</property> </property>
<property> <property>
<name>sparkExecutorCores</name> <name>sparkExecutorCores</name>
<description>number of cores used by single executor</description> <description>number of cores used by single executor</description>
</property> </property>
</parameters> </parameters>
<start to="DownloadEBILinks"/> <start to="DownloadEBILinks"/>
<kill name="Kill"> <kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message> <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill> </kill>
<action name="DownloadEBILinks"> <action name="DownloadEBILinks">
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master> <master>yarn-cluster</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Incremental Download EBI Links</name> <name>Incremental Download EBI Links</name>
<class>eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks</class> <class>eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores} --executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory} --driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners} --conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=2000 --conf spark.sql.shuffle.partitions=2000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg> <arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg> <arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn</arg> <arg>--master</arg><arg>yarn</arg>
</spark> </spark>
<ok to="End"/> <ok to="OverrideFolders"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>
<action name="OverrideFolders">
<end name="End"/> <fs>
</workflow-app> <delete path="${sourcePath}/ebi_links_dataset_old"/>
<move source="${sourcePath}/ebi_links_dataset" target="${sourcePath}/ebi_links_dataset_old"/>
<move source="${workingPath}/links_final" target="${sourcePath}/ebi_links_dataset"/>
</fs>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

3
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/BioScholixTest.scala
View File

@ -7,6 +7,7 @@ import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.ScholixResolved import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.ScholixResolved
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF
import eu.dnetlib.dhp.sx.graph.bio.pubmed.PubMedToOaf.dataInfo import eu.dnetlib.dhp.sx.graph.bio.pubmed.PubMedToOaf.dataInfo
import eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks
import org.json4s.DefaultFormats import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString} import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse import org.json4s.jackson.JsonMethods.parse
@ -50,6 +51,8 @@ class BioScholixTest extends AbstractVocabularyTest{
} }
@Test @Test
def testEBIData() = { def testEBIData() = {
val inputXML = Source.fromInputStream(getClass.getResourceAsStream("pubmed.xml")).mkString val inputXML = Source.fromInputStream(getClass.getResourceAsStream("pubmed.xml")).mkString

1433
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/ls_result Normal file
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File diff suppressed because it is too large Load Diff

2
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh
View File

@ -16,7 +16,7 @@ curl -L ${CONTEXT_API}/contexts/?type=ri,community -H "accept: application/json"
cat contexts.csv | cut -d , -f1 | xargs -I {} curl -L ${CONTEXT_API}/context/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split(":")[0]),\(.id),\(.label)"' > categories.csv cat contexts.csv | cut -d , -f1 | xargs -I {} curl -L ${CONTEXT_API}/context/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split(":")[0]),\(.id),\(.label)"' > categories.csv
cat categories.csv | cut -d , -f2 | sed 's/:/%3A/g'| xargs -I {} curl -L ${CONTEXT_API}/context/category/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split("::")[0])::\(.id|split("::")[1]),\(.id),\(.label)"' > concepts.csv cat categories.csv | cut -d , -f2 | sed 's/:/%3A/g'| xargs -I {} curl -L ${CONTEXT_API}/context/category/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split("::")[0])::\(.id|split("::")[1]),\(.id),\(.label)"' > concepts.csv
cat contexts.csv | sed 's/^\(.*\),\(.*\)/\1,\1::other,\2/' >> categories.csv cat contexts.csv | sed 's/^\(.*\),\(.*\)/\1,\1::other,\2/' >> categories.csv
cat categories.csv | grep -v ::other | sed 's/^.*,\(.*\),\(.*\)/\1,\1::other,\2/' >> concepts.csv cat categories.csv | sed 's/^.*,\(.*\),\(.*\)/\1,\1::other,\2/' >> concepts.csv
echo "uploading context data to hdfs" echo "uploading context data to hdfs"
hdfs dfs -mkdir ${TMP} hdfs dfs -mkdir ${TMP}

2
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/indicators.sh
View File

@ -15,5 +15,5 @@ hdfs dfs -copyToLocal $SCRIPT_PATH
echo "Creating indicators" echo "Creating indicators"
impala-shell -q "invalidate metadata" impala-shell -q "invalidate metadata"
impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/^\(.*\)/compute stats ${TARGET}.\1;/" | impala-shell -c -f - impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/^\(.*\)/compute stats ${TARGET}.\1;/" | impala-shell -c -f -
cat step16_7-createIndicatorsTables.sql | impala-shell -d $TARGET -f - cat step16-createIndicatorsTables.sql | impala-shell -d $TARGET -f -
echo "Indicators created" echo "Indicators created"

11
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/observatory.sh → dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/observatory-post.sh
View File

@ -9,16 +9,9 @@ fi
export SOURCE=$1 export SOURCE=$1
export TARGET=$2 export TARGET=$2
export SHADOW=$3 export SHADOW=$3
export SCRIPT_PATH=$4
echo "Getting file from " $4 impala-shell -q "invalidate metadata;"
hdfs dfs -copyToLocal $4 impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/\(.*\)/compute stats ${TARGET}.\1;/" | impala-shell -f -
echo "Creating observatory database"
impala-shell -q "drop database if exists ${TARGET} cascade"
impala-shell -q "create database if not exists ${TARGET}"
impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${TARGET}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -f -
cat step21-createObservatoryDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 | impala-shell -f -
echo "Impala shell finished" echo "Impala shell finished"
echo "Updating shadow observatory database" echo "Updating shadow observatory database"

16
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/observatory-pre.sh Normal file
View File

@ -0,0 +1,16 @@
export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs
export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami)
if ! [ -L $link_folder ]
then
rm -Rf "$link_folder"
ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
fi
export SOURCE=$1
export TARGET=$2
export SHADOW=$3
echo "Creating observatory database"
impala-shell -q "drop database if exists ${TARGET} cascade"
impala-shell -q "create database if not exists ${TARGET}"
impala-shell -d ${SOURCE} -q "show tables" --delimited | grep -iv roar | sed "s/\(.*\)/create view ${TARGET}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -f -

5
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql
View File

@ -23,6 +23,11 @@ CREATE OR REPLACE VIEW ${stats_db_name}.rndexpediture AS
SELECT * SELECT *
FROM ${external_stats_db_name}.rndexpediture; FROM ${external_stats_db_name}.rndexpediture;
CREATE OR REPLACE VIEW ${stats_db_name}.licenses_normalized AS
SELECT *
FROM ${external_stats_db_name}.licenses_normalized;
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
-- Creation date of the database -- Creation date of the database

0
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_6.sql → dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql
View File

48
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_7-createIndicatorsTables.sql → dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql
View File

@ -233,4 +233,50 @@ on p.id= tmp.id;
create table indi_pub_has_abstract stored as parquet as create table indi_pub_has_abstract stored as parquet as
select distinct publication.id, coalesce(abstract, 1) has_abstract select distinct publication.id, coalesce(abstract, 1) has_abstract
from publication; from publication;
create table indi_with_orcid stored as parquet as
select distinct r.id, coalesce(has_orcid, 0) as has_orcid
from result r
left outer join (select id, 1 as has_orcid from result_orcid) tmp
on r.id= tmp.id
create table indi_funded_result_with_fundref stored as parquet as
select distinct r.id, coalesce(fundref, 0) as fundref
from project_results r
left outer join (select distinct id, 1 as fundref from project_results
where provenance='Harvested') tmp
on r.id= tmp.id
create table indi_result_org_country_collab stored as parquet as
with tmp as
(select o.id as id, o.country , ro.id as result,r.type from organization o
join result_organization ro on o.id=ro.organization
join result r on r.id=ro.id where o.country <> 'UNKNOWN')
select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations
from tmp as o1
join tmp as o2 on o1.result=o2.result
where o1.id<>o2.id and o1.country<>o2.country
group by o1.id, o1.type,o2.country
create table indi_result_org_collab stored as parquet as
with tmp as
(select o.id, ro.id as result,r.type from organization o
join result_organization ro on o.id=ro.organization
join result r on r.id=ro.id)
select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaborations
from tmp as o1
join tmp as o2 on o1.result=o2.result
where o1.id<>o2.id
group by o1.id, o2.id, o1.type
create table indi_result_org_country_collab stored as parquet as
with tmp as
(select o.id as id, o.country , ro.id as result,r.type from organization o
join result_organization ro on o.id=ro.organization
join result r on r.id=ro.id where o.country <> 'UNKNOWN')
select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations
from tmp as o1
join tmp as o2 on o1.result=o2.result
where o1.id<>o2.id and o1.country<>o2.country
group by o1.id, o1.type,o2.country

62
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16.sql
View File

@ -1,62 +0,0 @@
----------------------------------------------------
-- Shortcuts for various definitions in stats db ---
----------------------------------------------------
-- Peer reviewed:
-- Results that have been collected from Crossref
create table ${stats_db_name}.result_peerreviewed as
with peer_reviewed as (
select distinct r.id as id
from ${stats_db_name}.result r
join ${stats_db_name}.result_sources rs on rs.id=r.id
join ${stats_db_name}.datasource d on d.id=rs.datasource
where d.name='Crossref')
select distinct peer_reviewed.id as id, true as peer_reviewed
from peer_reviewed
union all
select distinct r.id as id, false as peer_reviewed
from ${stats_db_name}.result r
left outer join peer_reviewed pr on pr.id=r.id
where pr.id is null;
-- Green OA:
-- OA results that are hosted by an Institutional repository and have NOT been harvested from a DOAJ journal.
create table ${stats_db_name}.result_greenoa as
with result_green as (
select distinct r.id as id
from ${stats_db_name}.result r
join ${stats_db_name}.result_datasources rd on rd.id=r.id
join ${stats_db_name}.datasource d on d.id=rd.datasource
left outer join (
select rd.id from ${stats_db_name}.result_datasources rd
join ${stats_db_name}.datasource d on rd.datasource=d.id
join ${stats_db_name}.datasource_sources sds on sds.id=d.id
join ${stats_db_name}.datasource sd on sd.id=sds.datasource
where sd.name='DOAJ-ARTICLES'
) as doaj on doaj.id=r.id
where r.bestlicence in ('Open Access', 'Open Source') and d.type='Institutional Repository' and doaj.id is null)
select distinct result_green.id, true as green
from result_green
union all
select distinct r.id as id, false as green
from ${stats_db_name}.result r
left outer join result_green rg on rg.id=r.id
where rg.id is null;
-- GOLD OA:
-- OA results that have been harvested from a DOAJ journal.
create table ${stats_db_name}.result_gold as
with result_gold as (
select distinct r.id as id
from ${stats_db_name}.result r
join ${stats_db_name}.result_datasources rd on rd.id=r.id
join ${stats_db_name}.datasource d on d.id=rd.datasource
join ${stats_db_name}.datasource_sources sds on sds.id=d.id
join ${stats_db_name}.datasource sd on sd.id=sds.datasource
where r.type='publication' and r.bestlicence='Open Access' and sd.name='DOAJ-Articles')
select distinct result_gold.id, true as gold
from result_gold
union all
select distinct r.id, false as gold
from ${stats_db_name}.result r
where r.id not in (select id from result_gold);

22
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql Normal file
View File

@ -0,0 +1,22 @@
----------------------------------------------------
-- Shortcuts for various definitions in stats db ---
----------------------------------------------------
-- Peer reviewed:
create table ${stats_db_name}.result_peerreviewed as
select r.id as id, case when doi.doi_from_crossref=1 and grey.grey_lit=0 then true else false end as peer_reviewed
from ${stats_db_name}.result r
left outer join ${stats_db_name}.indi_pub_doi_from_crossref doi on doi.id=r.id
left outer join ${stats_db_name}.indi_pub_grey_lit grey on grey.id=r.id;
-- Green OA:
create table ${stats_db_name}.result_greenoa as
select r.id, case when green.green_oa=1 then true else false end as green
from ${stats_db_name}.result r
left outer join ${stats_db_name}.indi_pub_green_oa green on green.id=r.id;
-- GOLD OA:
create table ${stats_db_name}.result_gold as
select r.id, case when gold.gold_oa=1 then true else false end as gold
from ${stats_db_name}.result r
left outer join ${stats_db_name}.indi_pub_gold_oa gold on gold.id=r.id;

41
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql
View File

@ -104,25 +104,42 @@ create table TARGET.project_results as select id as result, project as id from T
compute stats TARGET.project_results; compute stats TARGET.project_results;
-- indicators -- indicators
create table TARGET.indi_pub_green_oa as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); create view TARGET.indi_dataset_avg_year_content_oa as select * from SOURCE.indi_dataset_avg_year_content_oa orig;
compute stats TARGET.indi_pub_green_oa; create view TARGET.indi_dataset_avg_year_context_oa as select * from SOURCE.indi_dataset_avg_year_context_oa orig;
create table TARGET.indi_pub_grey_lit as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.indi_pub_grey_lit;
create table TARGET.indi_pub_doi_from_crossref as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.indi_pub_doi_from_crossref;
create table TARGET.indi_pub_gold_oa as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.indi_pub_gold_oa;
create view TARGET.indi_dataset_avg_year_country_oa as select * from SOURCE.indi_dataset_avg_year_country_oa orig; create view TARGET.indi_dataset_avg_year_country_oa as select * from SOURCE.indi_dataset_avg_year_country_oa orig;
create view TARGET.indi_other_avg_year_content_oa as select * from SOURCE.indi_other_avg_year_content_oa orig;
create view TARGET.indi_other_avg_year_context_oa as select * from SOURCE.indi_other_avg_year_context_oa orig;
create view TARGET.indi_other_avg_year_country_oa as select * from SOURCE.indi_other_avg_year_country_oa orig;
create view TARGET.indi_project_datasets_count as select * from SOURCE.indi_project_datasets_count orig; create view TARGET.indi_project_datasets_count as select * from SOURCE.indi_project_datasets_count orig;
create view TARGET.indi_project_otherresearch_count as select * from SOURCE.indi_project_otherresearch_count orig; create view TARGET.indi_project_otherresearch_count as select * from SOURCE.indi_project_otherresearch_count orig;
create view TARGET.indi_project_pubs_count as select * from SOURCE.indi_project_pubs_count orig; create view TARGET.indi_project_pubs_count as select * from SOURCE.indi_project_pubs_count orig;
create view TARGET.indi_project_software_count as select * from SOURCE.indi_project_software_count orig; create view TARGET.indi_project_software_count as select * from SOURCE.indi_project_software_count orig;
create view TARGET.indi_pub_avg_year_content_oa as select * from SOURCE.indi_pub_avg_year_content_oa orig;
create view TARGET.indi_pub_avg_year_context_oa as select * from SOURCE.indi_pub_avg_year_context_oa orig;
create view TARGET.indi_pub_avg_year_country_oa as select * from SOURCE.indi_pub_avg_year_country_oa orig; create view TARGET.indi_pub_avg_year_country_oa as select * from SOURCE.indi_pub_avg_year_country_oa orig;
create table TARGET.indi_pub_green_oa as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.indi_pub_green_oa;
create table TARGET.indi_pub_grey_lit as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.indi_pub_grey_lit;
create table TARGET.indi_pub_doi_from_crossref as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.indi_pub_doi_from_crossref;
create table TARGET.indi_pub_gold_oa as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.indi_pub_gold_oa;
create table TARGET.indi_pub_has_abstract as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.indi_pub_has_abstract;
create table TARGET.indi_pub_has_cc_licence as select * from SOURCE.indi_pub_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.indi_pub_has_cc_licence;
create table TARGET.indi_pub_has_cc_licence_url as select * from SOURCE.indi_pub_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.indi_pub_has_cc_licence_url;
create view TARGET.indi_software_avg_year_content_oa as select * from SOURCE.indi_software_avg_year_content_oa orig;
create view TARGET.indi_software_avg_year_context_oa as select * from SOURCE.indi_software_avg_year_context_oa orig;
create view TARGET.indi_software_avg_year_country_oa as select * from SOURCE.indi_software_avg_year_country_oa orig;
--denorm --denorm
alter table TARGET.result rename to TARGET.res_tmp; alter table TARGET.result rename to TARGET.res_tmp;

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dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql
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@ -1,259 +1,561 @@
create table TARGET.result_affiliated_country stored as parquet as create table ${observatory_db_name}.result_cc_licence stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select r.id, coalesce(rln.count, 0) > 0 as cc_licence
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, from ${stats_db_name}.result r
r.peer_reviewed, r.type, c.code as ccode, c.name as cname left outer join (
from SOURCE.result r select rl.id, sum(case when lower(rln.normalized) like 'cc-%' then 1 else 0 end) as count
join SOURCE.result_organization ro on ro.id=r.id from ${stats_db_name}.result_licenses rl
join SOURCE.organization o on o.id=ro.organization left outer join ${stats_db_name}.licenses_normalized rln on rl.type=rln.license
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' group by rl.id
left outer join SOURCE.result_licenses rl on rl.id=r.id ) rln on rln.id=r.id;
left outer join SOURCE.result_pids pids on pids.id=r.id
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, c.code, c.name;
create table TARGET.result_affiliated_year stored as parquet as create table ${observatory_db_name}.result_affiliated_country stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, r.peer_reviewed, r.type, r.year count(distinct r.id) as total,
from SOURCE.result r r.green,
join SOURCE.result_organization ro on ro.id=r.id r.gold,
join SOURCE.organization o on o.id=ro.organization case when rl.type is not null then true else false end as licence,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' case when pids.pid is not null then true else false end as pid,
left outer join SOURCE.result_licenses rl on rl.id=r.id case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
left outer join SOURCE.result_pids pids on pids.id=r.id r.peer_reviewed,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, r.year; rln.cc_licence,
r.abstract as abstract,
r.authors > 1 as multiple_authors,
rpc.count > 1 as multiple_projects,
rfc.count > 1 as multiple_funders,
r.type,
c.code as ccode, c.name as cname
from ${stats_db_name}.result r
join ${stats_db_name}.result_organization ro on ro.id=r.id
join ${stats_db_name}.organization o on o.id=ro.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, c.code, c.name;
create table TARGET.result_affiliated_year_country stored as parquet as create table ${observatory_db_name}.result_affiliated_year stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, count(distinct r.id) as total,
r.peer_reviewed, r.type, r.year, c.code as ccode, c.name as cname r.green,
from SOURCE.result r r.gold,
join SOURCE.result_organization ro on ro.id=r.id case when rl.type is not null then true else false end as licence,
join SOURCE.organization o on o.id=ro.organization case when pids.pid is not null then true else false end as pid,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
left outer join SOURCE.result_licenses rl on rl.id=r.id r.peer_reviewed,
left outer join SOURCE.result_pids pids on pids.id=r.id rln.cc_licence,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, r.year, c.code, c.name; r.abstract as abstract,
r.authors > 1 as multiple_authors,
rpc.count > 1 as multiple_projects,
rfc.count > 1 as multiple_funders,
r.type,
r.year
from ${stats_db_name}.result r
join ${stats_db_name}.result_organization ro on ro.id=r.id
join ${stats_db_name}.organization o on o.id=ro.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year;
create table TARGET.result_affiliated_datasource stored as parquet as create table ${observatory_db_name}.result_affiliated_year_country stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, r.peer_reviewed, r.type, d.name as dname count(distinct r.id) as total,
from SOURCE.result r r.green,
join SOURCE.result_organization ro on ro.id=r.id r.gold,
join SOURCE.organization o on o.id=ro.organization case when rl.type is not null then true else false end as licence,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' case when pids.pid is not null then true else false end as pid,
left outer join SOURCE.result_datasources rd on rd.id=r.id case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
left outer join SOURCE.datasource d on d.id=rd.datasource r.peer_reviewed,
left outer join SOURCE.result_licenses rl on rl.id=r.id rln.cc_licence,
left outer join SOURCE.result_pids pids on pids.id=r.id r.abstract as abstract,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, d.name; r.authors > 1 as multiple_authors,
rpc.count > 1 as multiple_projects,
rfc.count > 1 as multiple_funders,
r.type,
r.year, c.code as ccode, c.name as cname
from ${stats_db_name}.result r
join ${stats_db_name}.result_organization ro on ro.id=r.id
join ${stats_db_name}.organization o on o.id=ro.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year, c.code, c.name;
create table TARGET.result_affiliated_datasource_country stored as parquet as create table ${observatory_db_name}.result_affiliated_datasource stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, count(distinct r.id) as total,
r.peer_reviewed, r.type, d.name as dname, c.code as ccode, c.name as cname r.green,
from SOURCE.result r r.gold,
join SOURCE.result_organization ro on ro.id=r.id case when rl.type is not null then true else false end as licence,
join SOURCE.organization o on o.id=ro.organization case when pids.pid is not null then true else false end as pid,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
left outer join SOURCE.result_datasources rd on rd.id=r.id r.peer_reviewed,
left outer join SOURCE.datasource d on d.id=rd.datasource rln.cc_licence,
left outer join SOURCE.result_licenses rl on rl.id=r.id r.abstract as abstract,
left outer join SOURCE.result_pids pids on pids.id=r.id r.authors > 1 as multiple_authors,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, d.name, c.code, c.name; rpc.count > 1 as multiple_projects,
rfc.count > 1 as multiple_funders,
r.type,
d.name as dname
from ${stats_db_name}.result r
join ${stats_db_name}.result_organization ro on ro.id=r.id
join ${stats_db_name}.organization o on o.id=ro.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
left outer join ${stats_db_name}.result_datasources rd on rd.id=r.id
left outer join ${stats_db_name}.datasource d on d.id=rd.datasource
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name;
create table TARGET.result_affiliated_organization stored as parquet as create table ${observatory_db_name}.result_affiliated_datasource_country stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, count(distinct r.id) as total,
r.peer_reviewed, r.type, o.name as oname r.green,
from SOURCE.result r r.gold,
join SOURCE.result_organization ro on ro.id=r.id case when rl.type is not null then true else false end as licence,
join SOURCE.organization o on o.id=ro.organization case when pids.pid is not null then true else false end as pid,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
left outer join SOURCE.result_licenses rl on rl.id=r.id r.peer_reviewed,
left outer join SOURCE.result_pids pids on pids.id=r.id rln.cc_licence,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, o.name; r.abstract as abstract,
r.authors > 1 as multiple_authors,
rpc.count > 1 as multiple_projects,
rfc.count > 1 as multiple_funders,
r.type,
d.name as dname, c.code as ccode, c.name as cname
from ${stats_db_name}.result r
join ${stats_db_name}.result_organization ro on ro.id=r.id
join ${stats_db_name}.organization o on o.id=ro.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
left outer join ${stats_db_name}.result_datasources rd on rd.id=r.id
left outer join ${stats_db_name}.datasource d on d.id=rd.datasource
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name, c.code, c.name;
create table TARGET.result_affiliated_organization_country stored as parquet as create table ${observatory_db_name}.result_affiliated_organization stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, count(distinct r.id) as total,
r.peer_reviewed, r.type, o.name as oname, c.code as ccode, c.name as cname r.green,
from SOURCE.result r r.gold,
join SOURCE.result_organization ro on ro.id=r.id case when rl.type is not null then true else false end as licence,
join SOURCE.organization o on o.id=ro.organization case when pids.pid is not null then true else false end as pid,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
left outer join SOURCE.result_licenses rl on rl.id=r.id r.peer_reviewed,
left outer join SOURCE.result_pids pids on pids.id=r.id rln.cc_licence,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, o.name, c.code, c.name; r.abstract as abstract,
r.authors > 1 as multiple_authors,
rpc.count > 1 as multiple_projects,
rfc.count > 1 as multiple_funders,
r.type,
o.name as oname
from ${stats_db_name}.result r
join ${stats_db_name}.result_organization ro on ro.id=r.id
join ${stats_db_name}.organization o on o.id=ro.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name;
create table TARGET.result_affiliated_funder stored as parquet as create table ${observatory_db_name}.result_affiliated_organization_country stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, r.peer_reviewed, r.type, p.funder as pfunder count(distinct r.id) as total,
from SOURCE.result r r.green,
join SOURCE.result_organization ro on ro.id=r.id r.gold,
join SOURCE.organization o on o.id=ro.organization case when rl.type is not null then true else false end as licence,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' case when pids.pid is not null then true else false end as pid,
join SOURCE.result_projects rp on rp.id=r.id case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
join SOURCE.project p on p.id=rp.project r.peer_reviewed,
left outer join SOURCE.result_licenses rl on rl.id=r.id rln.cc_licence,
left outer join SOURCE.result_pids pids on pids.id=r.id r.abstract as abstract,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, p.funder; r.authors > 1 as multiple_authors,
rpc.count > 1 as multiple_projects,
rfc.count > 1 as multiple_funders,
r.type,
o.name as oname, c.code as ccode, c.name as cname
from ${stats_db_name}.result r
join ${stats_db_name}.result_organization ro on ro.id=r.id
join ${stats_db_name}.organization o on o.id=ro.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name, c.code, c.name;
create table TARGET.result_affiliated_funder_country stored as parquet as create table ${observatory_db_name}.result_affiliated_funder stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, count(distinct r.id) as total,
r.peer_reviewed, r.type, p.funder as pfunder, c.code as ccode, c.name as cname r.green,
from SOURCE.result r r.gold,
join SOURCE.result_organization ro on ro.id=r.id case when rl.type is not null then true else false end as licence,
join SOURCE.organization o on o.id=ro.organization case when pids.pid is not null then true else false end as pid,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
join SOURCE.result_projects rp on rp.id=r.id r.peer_reviewed,
join SOURCE.project p on p.id=rp.project rln.cc_licence,
left outer join SOURCE.result_licenses rl on rl.id=r.id r.abstract as abstract,
left outer join SOURCE.result_pids pids on pids.id=r.id r.authors > 1 as multiple_authors,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, p.funder, c.code, c.name; rpc.count > 1 as multiple_projects,
rfc.count > 1 as multiple_funders,
r.type,
p.funder as pfunder
from ${stats_db_name}.result r
join ${stats_db_name}.result_organization ro on ro.id=r.id
join ${stats_db_name}.organization o on o.id=ro.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
join ${stats_db_name}.result_projects rp on rp.id=r.id
join ${stats_db_name}.project p on p.id=rp.project
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder;
create table TARGET.result_deposited_country stored as parquet as create table ${observatory_db_name}.result_affiliated_funder_country stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, count(distinct r.id) as total,
r.peer_reviewed, r.type, c.code as ccode, c.name as cname r.green,
from SOURCE.result r r.gold,
join SOURCE.result_datasources rd on rd.id=r.id case when rl.type is not null then true else false end as licence,
join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository') case when pids.pid is not null then true else false end as pid,
join SOURCE.datasource_organizations dor on dor.id=d.id case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
join SOURCE.organization o on o.id=dor.organization r.peer_reviewed,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' rln.cc_licence,
left outer join SOURCE.result_licenses rl on rl.id=r.id r.abstract as abstract,
left outer join SOURCE.result_pids pids on pids.id=r.id r.authors > 1 as multiple_authors,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, c.code, c.name; rpc.count > 1 as multiple_projects,
rfc.count > 1 as multiple_funders,
r.type,
p.funder as pfunder, c.code as ccode, c.name as cname
from ${stats_db_name}.result r
join ${stats_db_name}.result_organization ro on ro.id=r.id
join ${stats_db_name}.organization o on o.id=ro.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
join ${stats_db_name}.result_projects rp on rp.id=r.id
join ${stats_db_name}.project p on p.id=rp.project
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder, c.code, c.name;
create table TARGET.result_deposited_year stored as parquet as create table ${observatory_db_name}.result_deposited_country stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, r.peer_reviewed, r.type, r.year count(distinct r.id) as total,
from SOURCE.result r r.green,
join SOURCE.result_datasources rd on rd.id=r.id r.gold,
join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository') case when rl.type is not null then true else false end as licence,
join SOURCE.datasource_organizations dor on dor.id=d.id case when pids.pid is not null then true else false end as pid,
join SOURCE.organization o on o.id=dor.organization case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' r.peer_reviewed,
left outer join SOURCE.result_licenses rl on rl.id=r.id rln.cc_licence,
left outer join SOURCE.result_pids pids on pids.id=r.id r.abstract as abstract,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, r.year; r.authors > 1 as multiple_authors,
rpc.count > 1 as multiple_projects,
rfc.count > 1 as multiple_funders,
r.type,
c.code as ccode, c.name as cname
from ${stats_db_name}.result r
join ${stats_db_name}.result_datasources rd on rd.id=r.id
join ${stats_db_name}.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
join ${stats_db_name}.datasource_organizations dor on dor.id=d.id
join ${stats_db_name}.organization o on o.id=dor.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, c.code, c.name;
create table TARGET.result_deposited_year_country stored as parquet as create table ${observatory_db_name}.result_deposited_year stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, count(distinct r.id) as total,
r.peer_reviewed, r.type, r.year, c.code as ccode, c.name as cname r.green,
from SOURCE.result r r.gold,
join SOURCE.result_datasources rd on rd.id=r.id case when rl.type is not null then true else false end as licence,
join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository') case when pids.pid is not null then true else false end as pid,
join SOURCE.datasource_organizations dor on dor.id=d.id case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
join SOURCE.organization o on o.id=dor.organization r.peer_reviewed,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' rln.cc_licence,
left outer join SOURCE.result_licenses rl on rl.id=r.id r.abstract as abstract,
left outer join SOURCE.result_pids pids on pids.id=r.id r.authors > 1 as multiple_authors,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, r.year, c.code, c.name; rpc.count > 1 as multiple_projects,
rfc.count > 1 as multiple_funders,
r.type,
r.year
from ${stats_db_name}.result r
join ${stats_db_name}.result_datasources rd on rd.id=r.id
join ${stats_db_name}.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
join ${stats_db_name}.datasource_organizations dor on dor.id=d.id
join ${stats_db_name}.organization o on o.id=dor.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year;
create table TARGET.result_deposited_datasource stored as parquet as create table ${observatory_db_name}.result_deposited_year_country stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, count(distinct r.id) as total,
r.peer_reviewed, r.type, d.name as dname r.green,
from SOURCE.result r r.gold,
join SOURCE.result_datasources rd on rd.id=r.id case when rl.type is not null then true else false end as licence,
join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository') case when pids.pid is not null then true else false end as pid,
join SOURCE.datasource_organizations dor on dor.id=d.id case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
join SOURCE.organization o on o.id=dor.organization r.peer_reviewed,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' rln.cc_licence,
left outer join SOURCE.result_licenses rl on rl.id=r.id r.abstract as abstract,
left outer join SOURCE.result_pids pids on pids.id=r.id r.authors > 1 as multiple_authors,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, d.name; rpc.count > 1 as multiple_projects,
rfc.count > 1 as multiple_funders,
r.type,
r.year, c.code as ccode, c.name as cname
from ${stats_db_name}.result r
join ${stats_db_name}.result_datasources rd on rd.id=r.id
join ${stats_db_name}.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
join ${stats_db_name}.datasource_organizations dor on dor.id=d.id
join ${stats_db_name}.organization o on o.id=dor.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year, c.code, c.name;
create table TARGET.result_deposited_datasource_country stored as parquet as create table ${observatory_db_name}.result_deposited_datasource stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, count(distinct r.id) as total,
r.peer_reviewed, r.type, d.name as dname, c.code as ccode, c.name as cname r.green,
from SOURCE.result r r.gold,
join SOURCE.result_datasources rd on rd.id=r.id case when rl.type is not null then true else false end as licence,
join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository') case when pids.pid is not null then true else false end as pid,
join SOURCE.datasource_organizations dor on dor.id=d.id case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
join SOURCE.organization o on o.id=dor.organization r.peer_reviewed,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' rln.cc_licence,
left outer join SOURCE.result_licenses rl on rl.id=r.id r.abstract as abstract,
left outer join SOURCE.result_pids pids on pids.id=r.id r.authors > 1 as multiple_authors,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, d.name, c.code, c.name; rpc.count > 1 as multiple_projects,
rfc.count > 1 as multiple_funders,
r.type,
d.name as dname
from ${stats_db_name}.result r
join ${stats_db_name}.result_datasources rd on rd.id=r.id
join ${stats_db_name}.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
join ${stats_db_name}.datasource_organizations dor on dor.id=d.id
join ${stats_db_name}.organization o on o.id=dor.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name;
create table TARGET.result_deposited_organization stored as parquet as create table ${observatory_db_name}.result_deposited_datasource_country stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, r.peer_reviewed, r.type, o.name as oname count(distinct r.id) as total,
from SOURCE.result r r.green,
join SOURCE.result_datasources rd on rd.id=r.id r.gold,
join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository') case when rl.type is not null then true else false end as licence,
join SOURCE.datasource_organizations dor on dor.id=d.id case when pids.pid is not null then true else false end as pid,
join SOURCE.organization o on o.id=dor.organization case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' r.peer_reviewed,
left outer join SOURCE.result_licenses rl on rl.id=r.id rln.cc_licence,
left outer join SOURCE.result_pids pids on pids.id=r.id r.abstract as abstract,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, o.name; r.authors > 1 as multiple_authors,
rpc.count > 1 as multiple_projects,
rfc.count > 1 as multiple_funders,
r.type,
d.name as dname, c.code as ccode, c.name as cname
from ${stats_db_name}.result r
join ${stats_db_name}.result_datasources rd on rd.id=r.id
join ${stats_db_name}.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
join ${stats_db_name}.datasource_organizations dor on dor.id=d.id
join ${stats_db_name}.organization o on o.id=dor.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name, c.code, c.name;
create table TARGET.result_deposited_organization_country stored as parquet as create table ${observatory_db_name}.result_deposited_organization stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, count(distinct r.id) as total,
r.peer_reviewed, r.type, o.name as oname, c.code as ccode, c.name as cname r.green,
from SOURCE.result r r.gold,
join SOURCE.result_datasources rd on rd.id=r.id case when rl.type is not null then true else false end as licence,
join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository') case when pids.pid is not null then true else false end as pid,
join SOURCE.datasource_organizations dor on dor.id=d.id case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
join SOURCE.organization o on o.id=dor.organization r.peer_reviewed,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' rln.cc_licence,
left outer join SOURCE.result_licenses rl on rl.id=r.id r.abstract as abstract,
left outer join SOURCE.result_pids pids on pids.id=r.id r.authors > 1 as multiple_authors,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, o.name, c.code, c.name; rpc.count > 1 as multiple_projects,
rfc.count > 1 as multiple_funders,
r.type,
o.name as oname
from ${stats_db_name}.result r
join ${stats_db_name}.result_datasources rd on rd.id=r.id
join ${stats_db_name}.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
join ${stats_db_name}.datasource_organizations dor on dor.id=d.id
join ${stats_db_name}.organization o on o.id=dor.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name;
create table TARGET.result_deposited_funder stored as parquet as create table ${observatory_db_name}.result_deposited_organization_country stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, count(distinct r.id) as total,
r.peer_reviewed, r.type, p.funder as pfunder r.green,
from SOURCE.result r r.gold,
join SOURCE.result_datasources rd on rd.id=r.id case when rl.type is not null then true else false end as licence,
join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository') case when pids.pid is not null then true else false end as pid,
join SOURCE.datasource_organizations dor on dor.id=d.id case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
join SOURCE.organization o on o.id=dor.organization r.peer_reviewed,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' rln.cc_licence,
join SOURCE.result_projects rp on rp.id=r.id r.abstract as abstract,
join SOURCE.project p on p.id=rp.project r.authors > 1 as multiple_authors,
left outer join SOURCE.result_licenses rl on rl.id=r.id rpc.count > 1 as multiple_projects,
left outer join SOURCE.result_pids pids on pids.id=r.id rfc.count > 1 as multiple_funders,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, p.funder; r.type,
o.name as oname, c.code as ccode, c.name as cname
from ${stats_db_name}.result r
join ${stats_db_name}.result_datasources rd on rd.id=r.id
join ${stats_db_name}.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
join ${stats_db_name}.datasource_organizations dor on dor.id=d.id
join ${stats_db_name}.organization o on o.id=dor.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name, c.code, c.name;
create table TARGET.result_deposited_funder_country stored as parquet as create table ${observatory_db_name}.result_deposited_funder stored as parquet as
select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence, select
case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, count(distinct r.id) as total,
r.peer_reviewed, r.type, p.funder as pfunder, c.code as ccode, c.name as cname r.green,
from SOURCE.result r r.gold,
join SOURCE.result_datasources rd on rd.id=r.id case when rl.type is not null then true else false end as licence,
join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository') case when pids.pid is not null then true else false end as pid,
join SOURCE.datasource_organizations dor on dor.id=d.id case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
join SOURCE.organization o on o.id=dor.organization r.peer_reviewed,
join SOURCE.country c on c.code=o.country and c.continent_name='Europe' rln.cc_licence,
join SOURCE.result_projects rp on rp.id=r.id r.abstract as abstract,
join SOURCE.project p on p.id=rp.project r.authors > 1 as multiple_authors,
left outer join SOURCE.result_licenses rl on rl.id=r.id rpc.count > 1 as multiple_projects,
left outer join SOURCE.result_pids pids on pids.id=r.id rfc.count > 1 as multiple_funders,
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, p.funder, c.code, c.name; r.type,
p.funder as pfunder
from ${stats_db_name}.result r
join ${stats_db_name}.result_datasources rd on rd.id=r.id
join ${stats_db_name}.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
join ${stats_db_name}.datasource_organizations dor on dor.id=d.id
join ${stats_db_name}.organization o on o.id=dor.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
join ${stats_db_name}.result_projects rp on rp.id=r.id
join ${stats_db_name}.project p on p.id=rp.project
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder;
compute stats TARGET.result_affiliated_country; create table ${observatory_db_name}.result_deposited_funder_country stored as parquet as
compute stats TARGET.result_affiliated_year; select
compute stats TARGET.result_affiliated_year_country; count(distinct r.id) as total,
compute stats TARGET.result_affiliated_datasource; r.green,
compute stats TARGET.result_affiliated_datasource_country; r.gold,
compute stats TARGET.result_affiliated_organization; case when rl.type is not null then true else false end as licence,
compute stats TARGET.result_affiliated_organization_country; case when pids.pid is not null then true else false end as pid,
compute stats TARGET.result_affiliated_funder; case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
compute stats TARGET.result_affiliated_funder_country; r.peer_reviewed,
compute stats TARGET.result_deposited_country; rln.cc_licence,
compute stats TARGET.result_deposited_year; r.abstract as abstract,
compute stats TARGET.result_deposited_year_country; r.authors > 1 as multiple_authors,
compute stats TARGET.result_deposited_datasource; rpc.count > 1 as multiple_projects,
compute stats TARGET.result_deposited_datasource_country; rfc.count > 1 as multiple_funders,
compute stats TARGET.result_deposited_organization; r.type,
compute stats TARGET.result_deposited_organization_country; p.funder as pfunder, c.code as ccode, c.name as cname
compute stats TARGET.result_deposited_funder; from ${stats_db_name}.result r
compute stats TARGET.result_deposited_funder_country; join ${stats_db_name}.result_datasources rd on rd.id=r.id
join ${stats_db_name}.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
join ${stats_db_name}.datasource_organizations dor on dor.id=d.id
join ${stats_db_name}.organization o on o.id=dor.organization
join ${stats_db_name}.country c on c.code=o.country and c.continent_name='Europe'
join ${stats_db_name}.result_projects rp on rp.id=r.id
join ${stats_db_name}.project p on p.id=rp.project
left outer join ${stats_db_name}.result_licenses rl on rl.id=r.id
left outer join ${stats_db_name}.result_pids pids on pids.id=r.id
left outer join ${observatory_db_name}.result_cc_licence rln on rln.id=r.id
left outer join ${stats_db_name}.result_projectcount rpc on rpc.id=r.id
left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder, c.code, c.name;

114
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
View File

@ -239,14 +239,51 @@
<param>stats_db_name=${stats_db_name}</param> <param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param> <param>openaire_db_name=${openaire_db_name}</param>
</hive2> </hive2>
<ok to="Step16"/> <ok to="Step15_5"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>
<action name="Step16"> <action name="Step15_5">
<hive2 xmlns="uri:oozie:hive2-action:0.1"> <hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url> <jdbc-url>${hive_jdbc_url}</jdbc-url>
<script>scripts/step16.sql</script> <script>scripts/step15_5.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
</hive2>
<ok to="Contexts"/>
<error to="Kill"/>
</action>
<action name="Contexts">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>contexts.sh</exec>
<argument>${context_api_url}</argument>
<argument>${stats_db_name}</argument>
<file>contexts.sh</file>
</shell>
<ok to="Step16-createIndicatorsTables"/>
<error to="Kill"/>
</action>
<action name="Step16-createIndicatorsTables">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>indicators.sh</exec>
<argument>${stats_db_name}</argument>
<argument>${wf:appPath()}/scripts/step16-createIndicatorsTables.sql</argument>
<file>indicators.sh</file>
</shell>
<ok to="Step16_1-definitions"/>
<error to="Kill"/>
</action>
<action name="Step16_1-definitions">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<script>scripts/step16_1-definitions.sql</script>
<param>stats_db_name=${stats_db_name}</param> <param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param> <param>openaire_db_name=${openaire_db_name}</param>
</hive2> </hive2>
@ -261,48 +298,11 @@
<param>stats_db_name=${stats_db_name}</param> <param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param> <param>openaire_db_name=${openaire_db_name}</param>
</hive2> </hive2>
<ok to="Step16_6"/> <ok to="Step19-finalize"/>
<error to="Kill"/>
</action>
<action name="Step16_6">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<script>scripts/step16_6.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
</hive2>
<ok to="Step16_7-createIndicatorsTables"/>
<error to="Kill"/>
</action>
<action name="Step16_7-createIndicatorsTables">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>indicators.sh</exec>
<argument>${stats_db_name}</argument>
<argument>${wf:appPath()}/scripts/step16_7-createIndicatorsTables.sql</argument>
<file>indicators.sh</file>
</shell>
<ok to="Step17"/>
<error to="Kill"/>
</action>
<action name="Step17">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>contexts.sh</exec>
<argument>${context_api_url}</argument>
<argument>${stats_db_name}</argument>
<file>contexts.sh</file>
</shell>
<ok to="Step19"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>
<action name="Step19"> <action name="Step19-finalize">
<shell xmlns="uri:oozie:shell-action:0.1"> <shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker> <job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node> <name-node>${nameNode}</name-node>
@ -326,20 +326,44 @@
<argument>${wf:appPath()}/scripts/step20-createMonitorDB.sql</argument> <argument>${wf:appPath()}/scripts/step20-createMonitorDB.sql</argument>
<file>monitor.sh</file> <file>monitor.sh</file>
</shell> </shell>
<ok to="step21-createObservatoryDB-pre"/>
<error to="Kill"/>
</action>
<action name="step21-createObservatoryDB-pre">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>observatory-pre.sh</exec>
<argument>${stats_db_name}</argument>
<argument>${observatory_db_name}</argument>
<argument>${observatory_db_shadow_name}</argument>
<file>observatory-pre.sh</file>
</shell>
<ok to="step21-createObservatoryDB"/> <ok to="step21-createObservatoryDB"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>
<action name="step21-createObservatoryDB"> <action name="step21-createObservatoryDB">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<script>scripts/step21-createObservatoryDB.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>observatory_db_name=${observatory_db_name}</param>
</hive2>
<ok to="step21-createObservatoryDB-post"/>
<error to="Kill"/>
</action>
<action name="step21-createObservatoryDB-post">
<shell xmlns="uri:oozie:shell-action:0.1"> <shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker> <job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node> <name-node>${nameNode}</name-node>
<exec>observatory.sh</exec> <exec>observatory-post.sh</exec>
<argument>${stats_db_name}</argument> <argument>${stats_db_name}</argument>
<argument>${observatory_db_name}</argument> <argument>${observatory_db_name}</argument>
<argument>${observatory_db_shadow_name}</argument> <argument>${observatory_db_shadow_name}</argument>
<argument>${wf:appPath()}/scripts/step21-createObservatoryDB.sql</argument> <file>observatory-post.sh</file>
<file>observatory.sh</file>
</shell> </shell>
<ok to="Step22"/> <ok to="Step22"/>
<error to="Kill"/> <error to="Kill"/>